GATK for mitochondrial dna mutations

Hi,
I was wondering whether it is possible to call low heteroplasmic variants with GATK. As many molecules of mtdna are present in one cell, you can find variants with a frequency of 1-100%. So I was wondering if I can detect variants of let say 4% using the GATK Unified genotyper?

Kind regards

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,

    A former collaborator of ours did some work on MT calling using UG with the generalized ploidy option. However he has moved on and the rest of us don't really have any experience doing this so we can't give you any recommendations, beyond saying that yes it is possible, but you'll need to play with the -ploidy settings to make it work.

    I hope this helps a little; maybe others will jump in with their recommendations.

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